package modeling;


/**
 * @author Mathieu Rousseau
 * @email mathieu.rousseau3@mail.mcgill.ca
 */


/** ------------------------------------------------------------------------------------------------------------------
 * start of MCMC5CTester class
 * ------------------------------------------------------------------------------------------------------------------  **/
public class MCMC5CTester {

	
	/*  start of main method  */
	public static void main(String[] args) {	

		//  parameters for the MCMC5C program
		String filenameIFs, filenameFragments;
		long runLength, numberOfStructuresToOutput;
		double stepSize, exponent;
		
		
		//  MCMC5C program object
//		MCMC5C structureSolver = new MCMC5C();
		
		
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		filenameIFs = "DMSO_experimental.txt";
//		filenameIFs = "PMA_experimental.txt";
		filenameFragments = "fragments.txt";

//		filenameIFs = "HiC_chr14_chr14.txt";
//		filenameFragments = "HiC_fragments.txt";

		runLength = (long)1E7;

		numberOfStructuresToOutput = 0;

		stepSize = 0.05;
		
		exponent = 2;

		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								END OF HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		
		//  add all of the parameters to the arguments array
		args = new String[6];
		args[0] = filenameIFs;
		args[1] = filenameFragments;
		args[2] = String.valueOf(runLength);
		args[3] = String.valueOf(numberOfStructuresToOutput);
		args[4] = String.valueOf(stepSize);
//		args[5] = String.valueOf(exponent);

		
		
		MCMC5C MCMC5CProgram;
		
		for(int i = 31; i <= 56; i++){
			
			MCMC5CProgram = new MCMC5C();
			
			double exponentValue = i / 10.0;
			args[5] = String.valueOf(exponentValue);
			
			MCMC5CProgram.run(args);
			
			MCMC5CProgram = null;
		}
		
		
		
		//  run the MCMC5C program
//		structureSolver.run(args);
		
	}/*  end of main method  */

	
}/*  end of MCMC5CTester class  */